Hybrid squaraine-SiO 2 nanoparticles extremely homogeneous in size (50 ± 2 nm), and with photoluminescent emission in the optical tissue window, were prepare by using the reverse microemulsion technique. Three different high quantum-yield squaraine dyes were used and the photophysical behavior of the prepared samples were qualitatively and quantitatively studied, by steady state and time-resolved photoluminescence, in order to establish structure-property relationships useful for the optimization of the preparation method. These squaraine dyes are insoluble in water and suffer a severe decrease of quantum yield if derivatized with polar groups. The role of the hydrophilicity of the dye-APTS adduct in ruling its dispersion in the nascent silica matrix was confirmed, and the possibility to improve the tuning of the process by properly administration of the adduct with the co-surfactant was demonstrated.